Gene expression profile at a single-cell level of CD45+ cells from the livers of mice hepatocellular carcinoma (HCC).

We used droplet-based scRNA-seq to profile the gene expression of magnetically-sorted CD45+ T cells from the livers of helathy mice and mice with HCC. Overall design: Two million liver CD45+ cells from each mouse were individually labeled with cell multiplexing oligos (CMOs, 10X Genomics) to allow for the multiplexing of individual samples prior to pooling and gel bead-in-emulsion (GEM) preparation. Separate gene expression and CMO libraries were created and sequenced in a Novaseq S4 chip (2 x 150bp PE).